I have issues while running python setup.py test, with glpksol in the $PATH:
An idea?
Regards
running test
running egg_info
writing requirements to gim3e.egg-info/requires.txt
writing gim3e.egg-info/PKG-INFO
writing top-level names to gim3e.egg-info/top_level.txt
writing dependency_links to gim3e.egg-info/dependency_links.txt
reading manifest file 'gim3e.egg-info/SOURCES.txt'
writing manifest file 'gim3e.egg-info/SOURCES.txt'
running build_ext
/software/lib64/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
test_convert_objective_to_constraint (gim3e.test.unit_tests.TestGim3eCore) ... ERROR
test_convert_to_irreversible (gim3e.test.unit_tests.TestGim3eCore) ... cobra/core/Reaction.py:192 UserWarning: Setting reaction reversibility is ignored
ERROR
test_evaluate_penalties (gim3e.test.unit_tests.TestGim3eCore) ... ERROR
test_irreversible_flux_variability_analysis (gim3e.test.unit_tests.TestGim3eCore) ... ERROR
test_optimize_turnover_metabolite (gim3e.test.unit_tests.TestGim3eCore) ... ERROR
test_solve_feasible (gim3e.test.unit_tests.TestGim3eCore) ... ERROR
test_solve_milp_feasible (gim3e.test.unit_tests.TestGim3eCore) ... ERROR
Traceback (most recent call last):
File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 131, in test_convert_to_irreversible
gene_from_reaction = [x.id for x in the_reaction.get_gene()]
AttributeError: 'Reaction' object has no attribute 'get_gene'
Traceback (most recent call last):
File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 73, in test_solve_milp_feasible
tolerance_integer = gim3e.integer_tolerances[the_solver]
KeyError: None
Ran 7 tests in 1.929s
FAILED (errors=7)
No working solvers detected.
No working solvers detected.
No working solvers detected.
No working solvers detected.
No working solvers detected.
No working solvers detected.
Hi
I have issues while running python setup.py test, with glpksol in the $PATH: An idea?
Regards
running test running egg_info writing requirements to gim3e.egg-info/requires.txt writing gim3e.egg-info/PKG-INFO writing top-level names to gim3e.egg-info/top_level.txt writing dependency_links to gim3e.egg-info/dependency_links.txt reading manifest file 'gim3e.egg-info/SOURCES.txt' writing manifest file 'gim3e.egg-info/SOURCES.txt' running build_ext /software/lib64/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment. warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.') test_convert_objective_to_constraint (gim3e.test.unit_tests.TestGim3eCore) ... ERROR test_convert_to_irreversible (gim3e.test.unit_tests.TestGim3eCore) ... cobra/core/Reaction.py:192 UserWarning: Setting reaction reversibility is ignored ERROR test_evaluate_penalties (gim3e.test.unit_tests.TestGim3eCore) ... ERROR test_irreversible_flux_variability_analysis (gim3e.test.unit_tests.TestGim3eCore) ... ERROR test_optimize_turnover_metabolite (gim3e.test.unit_tests.TestGim3eCore) ... ERROR test_solve_feasible (gim3e.test.unit_tests.TestGim3eCore) ... ERROR test_solve_milp_feasible (gim3e.test.unit_tests.TestGim3eCore) ... ERROR
ERROR: test_convert_objective_to_constraint (gim3e.test.unit_tests.TestGim3eCore)
Traceback (most recent call last): File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 156, in test_convert_objective_to_constraint tolerance_integer = gim3e.integer_tolerances[the_solver] KeyError: None
ERROR: test_convert_to_irreversible (gim3e.test.unit_tests.TestGim3eCore)
Traceback (most recent call last): File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 131, in test_convert_to_irreversible gene_from_reaction = [x.id for x in the_reaction.get_gene()] AttributeError: 'Reaction' object has no attribute 'get_gene'
ERROR: test_evaluate_penalties (gim3e.test.unit_tests.TestGim3eCore)
Traceback (most recent call last): File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 212, in test_evaluate_penalties tolerance_integer = gim3e.integer_tolerances[the_solver] KeyError: None
ERROR: test_irreversible_flux_variability_analysis (gim3e.test.unit_tests.TestGim3eCore)
Traceback (most recent call last): File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 187, in test_irreversible_flux_variability_analysis tolerance_integer = gim3e.integer_tolerances[the_solver] KeyError: None
ERROR: test_optimize_turnover_metabolite (gim3e.test.unit_tests.TestGim3eCore)
Traceback (most recent call last): File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 92, in test_optimize_turnover_metabolite tolerance_integer = gim3e.integer_tolerances[the_solver] KeyError: None
ERROR: test_solve_feasible (gim3e.test.unit_tests.TestGim3eCore)
Traceback (most recent call last): File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 55, in test_solve_feasible tolerance_integer = gim3e.integer_tolerances[the_solver] KeyError: None
ERROR: test_solve_milp_feasible (gim3e.test.unit_tests.TestGim3eCore)
Traceback (most recent call last): File "/builddir/build/BUILD/gim3e-master/gim3e/test/unit_tests.py", line 73, in test_solve_milp_feasible tolerance_integer = gim3e.integer_tolerances[the_solver] KeyError: None
Ran 7 tests in 1.929s
FAILED (errors=7) No working solvers detected. No working solvers detected. No working solvers detected. No working solvers detected. No working solvers detected. No working solvers detected.
Python 2.7.5 COBRApy 0.4.1 glpk 4.59.1